Question: Trinity : average transcript size check + quality assessment
0
gravatar for iamtuttu5
3.3 years ago by
iamtuttu540
United States
iamtuttu540 wrote:

Hello all

 

I have performed trinity assembly , now i want assess the quality of the the assembled transcript .. with the most closely related species of my plant

I have created database of annotated reference transcriptome

tuttu@kau:~/ngs/trinityrnaseq-2.1.1$ makeblastdb -in test.fasta -dbtype nucl


Building a new DB, current time: 12/09/2015 17:59:24
New DB name:   test.fasta
New DB title:  test.fasta
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 61538 sequences in 4.21683 seconds.

 

After that i tried to run megablast to align the known transcripts to the Trinity assembly:

This is the command used :

blastn -query ~/ngs/trinityrnaseq-2.1.1/trinity_output_data2/Trinity.fasta -db /home/jinu/ngs/trinityrnaseq-2.1.1/test.fasta -out Trinity_vs_test.blastn -evalue 1e-20 -dust no -task megablast -num_threads 2 -max_target_seqs 1 -outfmt 6

 

But my attempt was unsuccessful

it results in this errorr

commmand line argument error: Argument "out". File is not accessible:  `test.blastn'

 

Thank you

 

rna-seq ngs assembly megablast • 1.4k views
ADD COMMENTlink written 3.3 years ago by iamtuttu540
1

Have you read An Error By Using Ncbi-Blast-2.2.25+ (On Windows) post? In that case the issue was related to incorrect dashes in blast arguments due to the copy/paste of command.

ADD REPLYlink written 3.3 years ago by iraun3.5k

I already gone through that post ... but still its not working for me

ADD REPLYlink written 3.3 years ago by iamtuttu540
1

For other hand I guess that the file which is not accessible is 'Trinity_vs_test.blastn', isn't it? Because 'test.blastn' is not specified in your command line..

ADD REPLYlink written 3.3 years ago by iraun3.5k

Also the error could be related to permissions problem that prevents writing to a file in the given folder. Have you check it?

ADD REPLYlink written 3.3 years ago by iraun3.5k

how to check that ?

ADD REPLYlink written 3.3 years ago by iamtuttu540

ls -lh command to see permissions, Then you can use chmod to change them. If you are not able to do it, google has a lot of examples related to permissions issues :).

ADD REPLYlink written 3.3 years ago by iraun3.5k

Thank you iraun let me try

ADD REPLYlink written 3.3 years ago by iamtuttu540
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